Eyespot, caused by the related fungal pathogens Oculimacula acuformis and O. yallundae, is an important cereal stem-base disease in temperate parts of the world. Both species are dispersed mainly by splash-dispersed conidia but are also known to undergo sexual reproduction, yielding apothecia containing ascospores. Field diagnosis of eyespot can be challenging, with other pathogens causing similar symptoms, which complicates eyespot management strategies. Differences between O. acuformis and O. yallundae (e.g., host pathogenicity and fungicide sensitivity) require that both be targeted for effective disease management. Here, we develop and apply two molecular methods for species-specific and mating-type (MAT1-1 or MAT1-2) discrimination of O. acuformis and O. yallundae isolates. First, a multiplex PCR-based diagnostic assay targeting the MAT idiomorph region was developed, allowing simultaneous determination of both species and mating type. This multiplex PCR assay was successfully applied to type a global collection of isolates. Second, the development of loop-mediated isothermal amplification (LAMP) assays targeting β-tubulin sequences, which allow fast (<9 min) species-specific discrimination of global O. acuformis and O. yallundae isolates, is described. The LAMP assay can detect very small amounts of target DNA (1 pg) and was successfully applied in planta. In addition, mating-type-specific LAMP assays were also developed for rapid (<12 min) genotyping of O. acuformis and O. yallundae isolates. Finally, the multiplex PCR-based diagnostic was applied, in conjunction with spore trapping in field experiments, to provide evidence of the wind dispersal of ascospores from a diseased crop. The results indicate an important role of the sexual cycle in the dispersal of eyespot.

Results from a series of crop sequence and single-year experiments that tested different straw and cultivation treatments in a total of 11 site-season combinations confirmed previous evidence that the development of eyespot disease in cereals can be decreased by debris in the seed bed even if that debris includes eyespot-infected stem bases, which are the principal sources of primary inoculum. Two of the experiments, which followed non-cereal break crops and tested the effects of crop debris applied after ploughing or tining on eyespot in winter wheat that was artificially inoculated with Oculimacula spp., provided convincing evidence that the effects can be attributed to the debris per se, and not to any associated husbandry practices. There were often larger effects on disease in summer than in spring or on severity than on incidence suggesting that the effects of debris cannot be explained solely by effects on inoculum or initial infection, and that debris has a disease-suppressive effect.

Summary A methodological molecular procedure, which included extraction and cloning of the ITS1/2 rDNA of root‐associated organisms with subsequent transformation and sequencing of representative clones, was effective for detection, discrimination and determination of the frequency of the main damping‐off pathogens in roots of Pinus sylvestris seedlings growing in different forest‐tree nursery soils and exhibiting different rates of disease progress. Roots exhibiting slower damping‐off progression were colonized by Fusarium oxysporum , Neonectria radicicola (Ascomycota) and Pythium spp. (Oomycota), which comprised 50% of the microbial community. Roots exhibiting faster damping‐off progression were dominated by Thanatephorus cucumeris (Basidiomycota), which comprised 80% of the microbial community . The microbial community was more diverse in roots with slower damping‐off progression (14 species) than in roots with faster disease progression (seven species).

A new species, Galactomyces britannicum (IMI395371, MycoBank 511261), is described from the roots of wheat in the UK. Dendryphion penicillatum var. sclerotiale, Fusariella indica, Pseudogymnoascus appendiculatus and Volucrispora graminea are reported for the first time from roots, rhizosphere or stem bases of wheat in the UK. A microconidiogenus synanamorph is described for V graminea and the species is epitypified to reflect this amendment.

Seed treatments containing fluquinconazole, silthiofam or a standard fungicide mixture with no activity against take-all were compared in all combinations of sequences in successive second and third winter wheat crops in five field experiments and second to fourth crops in a sixth experiment. Compared with the standard treatment, silthiofam decreased take-all more effectively than fluquinconazole when crops were sampled at tillering. In samples taken in summer, during grain filling, silthiofam often decreased the incidence of take-all (percentage of plants with root symptoms) more than fluquinconazole, but fluquinconazole more effectively decreased the incidence of severe take-all (percentage of plants with more than 75% of their root systems blackened). It is suggested that these differences are a consequence of more effective control of primary infection of roots by silthiofam and of secondary, root-to-root, infection by fluquinconazole. Silthiofam usually increased yield more than did fluquinconazole, perhaps as a consequence of better early protection during tiller and/or spikelet formation. Treatment with either of the fungicides affected epidemic development in the treated crop and in crops grown subsequently. In particular, decreased take-all had the effect of delaying the year-to-year epidemic, so that nontreatment of a subsequent crop resulted in an upsurge in disease. Treatment with either take-all fungicide of a crop grown after a treated crop was relatively effective if the epidemic in the comparable nontreated crop sequence was continuing to increase. It was, however, detrimental if the disease was approaching its peak in the first treated crop, particularly if a treated (fourth wheat) crop was being compared with a similar crop in a nontreated sequence in which take-all decline had developed. These results provide a basis for recommendations for the use of seed treatment fungicides in sequences of wheat crops.

The effects of tillage (ploughing vs minimum tillage) and application of chopped maize stalks on winter wheat cv. Hereward by Fusarium culmorum and F. graminearum were investigated in two 2‐year experiments in eastern England. Supplementary inoculum of each fungus (five isolates) was applied to the ground to the first wheat crop in each experiment. Infection of shoot bases (spring), stem bases (summer) and harvested grain were determined by isolating the fungi on agar media and by quantitative PCR. Stem bases were infected more frequently by F. culmorum (up to 35% where inoculum was applied) than F. graminearum (up to 22% where inoculum applied; otherwise scarce). Despite mist‐irrigation to encourage ear infection, the incidence of pathogens in grain was usually low, always less than 4% for F. culmorum, but up to 30% for F. graminearum where inoculum was applied to the ground. Lack of rainfall probably limited the dispersal of conidia from the ground to the ears. Ascospores, produced by F. graminearum (Gibberella zeae) but not F. culmorum, are less dependent on rainfall for dispersal. Infection of grains by F. graminearum was usually correlated significantly with stem infection and sometimes, negatively, with grain yield. Both conidia and ascospores were produced on the previous crop's debris, apparently in small amounts, throughout much of the year. Little horizontal (plot to plot) dispersal was evident. Non‐inversion cultivation and maize‐stalk amendments tended to decrease stem‐base disease, presumably through the effects of microbial antagonism or competition. However, the incidence of F. graminearum was increased in stem bases where maize stalks were present and in grain by both the presence of maize stalks and minimum tillage. The results support experimental data and UK survey data that non‐inversion tillage increases the risk of ear infection, especially by F. graminearum, and hence of mycotoxin contamination of grain. Maize presents an additional risk where weather conditions do not limit the proliferation of the pathogens. This is consistent with evidence from surveys that the region in which the wheat crop is grown is the main risk factor for ear infection and mycotoxin accumulation in grain.

Take-all disease (Gaeumannomyces graminis var. tritici) in wheat crops is known to be suppressed by naturally occurring antagonistic fungi, closely related to the pathogen, that infect grasses and cereals. This form of suppression was re-investigated because of the changing importance and role of grass weeds and grass covers in arable farming. Natural populations of the competitive fungus Gaeumannomyces cylindrosporus, allowed to develop under rye-grass, were more effective than artificially introduced populations in suppressing the development of take-all in following wheat crops. To be effective, the antagonist needs to be present before the start of wheat cropping. Introducing G. cylindrosporus, but not G. graminis var. graminis (a potential antagonist that is faster growing), into a previous crop, or just after the previous crop, sometimes suppressed take-all, but the effect was small. It is concluded that, for any future attempts at biocontrol by these fungi, they should be introduced into a preceding crop not susceptible to take-all. Take-all inoculum in the soil should be at a minimum and effective hosts of the take-all pathogen must not be present as weeds or volunteers.

Fusarium avenaceum, F. graminearum, F. poae and F. tricinctum showed abnormal growth, morphology and conidiation, and a tendency to produce crystals, inclusion bodies and sclerotia when freshly isolated from wheat stem bases or kernels onto low-carbon potato dextrose agar (PDA). Observations of alterations in conidiation and conidium morphology are particularly significant, as these are the principal morphological diagnostic characteristics for Fusarium species. The fungi had normal growth when sub-cultured onto standard PDA, suggesting that a balance of nutrients was responsible for the effects. Specific causes are discussed in detail in relation to published information. The importance of standard media in the identification of Fusarium species is emphasized, whilst non-standard media may be useful for specific purposes, including routine isolation of fungi from mixed communities of species with different nutrient requirements.

Grass species were grown in plots, as pure stands or mixed with wheat, after a sequence of wheat crops in which take-all (Gaeumannomyces graminis var. tritici) had developed. Annual brome grasses maintained take-all inoculum in the soil as well as wheat (grown as a continuous sequence), and much better than cultivated species with a perennial habit. Take-all developed more in wheat grown after Anisantha sterilis (barren brome) or Bromus secalinus (rye brome), with or without wheat, than in continuous grass-free wheat in the same year, where take-all decline was apparently occurring. It was equally or more severe, however, in wheat grown after Lolium perenne (rye-grass) or Festuca arundinacea (tall fescue), despite these species having left the least inoculum in the soil. It was most severe in plots where these two grasses had been grown as mixtures with wheat. It is postulated that the presence of these grasses inhibited the development of take-all-suppressive microbiota that had developed in the grass-free wheat crops. The effects of the grasses appeared to be temporary, as amounts of take-all in a second subsequent winter wheat test crop were similar after all treatments. These results have important implications for take-all risk in wheat and, perhaps, other cereal crops grown after grass weed-infested cereals or after set-aside or similar 1-year covers containing weeds or sown grasses, especially in combination with cereal volunteers. They also indicate that grasses might be used experimentally in wheat crop sequences for investigating the mechanisms of suppression of, and conduciveness to, take-all.

A seed treatment containing fluquinconazole as the only active ingredient was tested in sequences of up to six consecutive crops of winter wheat. It was applied or not applied in each year, and was tested in all possible combinations with treatments applied in previous years. Take-all was controlled effectively, and grain yield usually increased, when the disease intensity was moderate or severe in non-treated crops, but control of the most severe take-all did not result in acceptable yields or grain quality. Treatment of a first wheat or second wheat with little take-all did not usually benefit the subsequent crop. Non-treatment of a crop grown after a treated, diseased crop usually resulted in a marked increase in disease, indicating that treatment had delayed progress of the epidemic. Take-all was controlled by treatment of a crop grown after a treated, diseased crop but the amount of control and of increased yield was often less than that in a treated crop grown after a non-treated crop in the same crop sequence. Similar effects of seed treatment were apparent in crops grown on a site with take-all decline. The alternative fungicide, silthiofam, applied as a seed treatment in the later years of some experiments, was usually as effective as fluquinconazole. From these experiments, it is recommended that: a) fluquinconazole seed treatment should be applied to a second or third wheat crop, grown after a first wheat crop that was managed to avoid rapid take-all development (e.g. by avoiding very early sowing); b) a break crop should follow the treated crop; c) the seed treatment should not normally be used in longer sequences of wheat or on take-all decline soil unless it is planned to follow the treated crop with a non-cereal break.

A series of field experiments, each with a minimum of five consecutively grown crops of winter wheat, was used to study responses to fluquinconazole seed treatment applied at different stages in the development of take-all epidemics, including take-all decline. The results form the basis of recommendations for using fluquinconazole seed treatment for managing take-all in sequences of wheat crops.

The progress of development of stem-base pathogens in crops of second winter wheat was plotted in nine experiments in three years. The amount of each pathogen present was determined by quantitative PCR. Where Tapesia yallundae was present in quantifiable amounts, it usually developed earlier than the other eyespot pathogen, T. acuformis. Both species were usually present in greater amounts on cultivars which are more susceptible to eyespot. The sharp eyespot pathogen, Rhizoctonia cerealis, developed more erratically than either of the Tapesia spp. and there were no consistent effects on different cultivars. Fusarium spp., the cause of brown foot rot, were rarely present in quantifiable amounts, but Microdochium nivale was usually present as one or both of the varieties nivale and majus. Late-season (after anthesis) decreases in M. nivale suggest that any brown foot rot symptoms attributable to this fungus would have fully developed earlier. Cultivar differences in amounts of M. nivale were most clear in stems during internode extension and when relatively large amounts of DNA were present. Such differences approximately reflected eyespot susceptibility, cv. Soissons containing most and cv. Lynx containing least DNA. The results emphasise the difficulty in relating diagnoses, by quantitative PCR or other means, at early growth stages when decisions to apply fungicides against stem-base disease are made, to later disease severity.

Effects of regular treatments with the fungicides carbendazim and prochloraz applied to whole plots divided into subplots with different initial population mixtures of carbendazim‐sensitive or carbendazim‐resistantTapesia yallundaeorT. acuformiswere studied in successive crops of winter wheat from 1984/85 to 1999/2000. In unsprayed and carbendazim‐sprayed whole plots, a stable coexistence of about 50% each ofT. yallundaeandT. acuformisdeveloped within five seasons, but in whole plots sprayed with prochloraz or prochloraz plus carbendazim, the proportion ofT. acuformisincreased to > 80%. A discrete time difference equation model was derived from knowledge of the biology of eyespot and competition theory to describe the population changes. The model was fitted to the data from treatments where coexistence occurred [subplots in unsprayed (1985–92) and carbendazim‐sprayed (1985–89) whole plots], using nonlinear least squares regression. The optimized value of the resource overlap coefficient was small, suggesting niche differences between the two species. Populations were nearly 100% carbendazim‐resistant in carbendazim‐sprayed whole plots by July 1985 (one season) and in whole plots sprayed with prochloraz plus carbendazim by July 1986 (two seasons). In prochloraz‐sprayed whole plots, the proportion of carbendazim‐resistant isolates decreased more rapidly than in unsprayed whole plots in the 1980s, but by July 1992 a shift in populations in unsprayed and prochloraz‐sprayed whole plots towards predominantly carbendazim‐resistant strains had occurred.

Strains of fungi, including non-pathogenic Fusarium spp., were tested in control led-environment and field experiments for their ability to control the most important pathogenic and toxigenic Fusarium spp. that cause ear blight on cereals. They were tested at both the inoculum production and ear infection stages. Some fungi effectively decreased growth of Fusarium spp. on wheat straw and maize stem pieces (representing an inoculum source for ear or cob blight). The most effective of these were fungi (mainly non-Fusarium spp.) that had only small effects against F culmorum at the ear infection stage on barley, oats or wheat. Isolates of non-pathogenic Fusarium spp. were more effective against ear infection, however, decreasing ear blight and deoxynivalenol in the harvested grain as much as the standard fungicide, tebuconazole. Experiments to test for control at these two stages in the disease cycle are continuing.

Relationships between the incidence and severity of brown foot rot and of pathogenic fungi, determined by diagnostic and quantitative PCR, were investigated during the growth of nine winter wheat crops in three cropping seasons. Microdochium nivale vars nivale and majus were the only brown foot rot pathogens present in significant amounts. Relationships between disease symptoms and amounts of pathogen DNA were often weak in early spring (when shoot-base symptoms are usually most difficult to ascribe to particular pathogens by visual examination) because of indistinct symptoms and small amounts of pathogen. Relationships were strongest during stem elongation. The amount of M. nivale in the tissues tended to decline in the summer as the plants matured, apparently disappearing partially from necrotic lesions to which it contributed, resulting in a weakened relationship between symptoms and pathogen DNA. Regression analyses of brown foot rot on amounts of M. nivale DNA for different wheat cultivars generally produced lines with similar slopes but were often most significant for the cultivar with most eyespot resistance (i.e. with least confounding eyespot) or most apparently genuine brown foot rot. DNA of Fusarium spp. was rarely present in amounts sufficient to quantify.

The possibility that the Coemansia spiralis complex contains three species is discussed on the basis of six descriptions. The name C. spiralis is retained for the fungus first described with the appropriate generic placement and incorporates C. nantahalensis. The second species, for which preserved material is not available, is named as C. bainieri nom. nov., and C. linderi sp. nov. is the third species.